Changeset 12165 for NEMO/branches/2019/dev_ASINTER-01-05_merged/src/TOP/README.rst

Timestamp:

2019-12-11T09:27:27+01:00 (4 years ago)

Author:

davestorkey

Message:

2019/dev_ASINTER-01-05_merged: Update to r12072 of trunk.

File:

• NEMO/branches/2019/dev_ASINTER-01-05_merged/src/TOP/README.rst (modified) (7 diffs)

NEMO/branches/2019/dev_ASINTER-01-05_merged/src/TOP/README.rst

@@ -3 +3 @@
 ***************
 
+.. todo::
+
+
+
 .. contents::
-   :local:
-
-TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward biogeochemical models and
-provide the physical constraints/boundaries for oceanic tracers.
-It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules.
+   :local:
+
+TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward
+biogeochemical models and provide the physical constraints/boundaries for oceanic tracers.
+It consists of a modular framework to handle multiple ocean tracers,
+including also a variety of built-in modules.
 
 This component of the NEMO framework allows one to exploit available modules (see below) and
 further develop a range of applications, spanning from the implementation of a dye passive tracer to
 evaluate dispersion processes (by means of MY_TRC), track water masses age (AGE module),
-assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs),
-up to the full set of equations involving marine biogeochemical cycles.
+assess the ocean interior penetration of persistent chemical compounds
+(e.g., gases like CFC or even PCBs), up to the full set of equations involving
+marine biogeochemical cycles.
 
 Structure
 =========
 
-TOP interface has the following location in the source code ``./src/MBG/`` and
+TOP interface has the following location in the source code :file:`./src/TOP` and
 the following modules are available:
 
-``TRP``
-   Interface to NEMO physical core for computing tracers transport
-
-``CFC``
-   Inert carbon tracers (CFC11,CFC12,SF6)
-
-``C14``
-   Radiocarbon passive tracer
-
-``AGE``
-   Water age tracking
-
-``MY_TRC``
-   Template for creation of new modules and external BGC models coupling
-
-``PISCES``
-   Built in BGC model.
-   See [https://www.geosci-model-dev.net/8/2465/2015/gmd-8-2465-2015-discussion.html Aumont et al. (2015)] for
-   a throughout description. |
-
-The usage of TOP is activated i) by including in the configuration definition  the component ``MBG`` and
-ii) by adding the macro ``key_top`` in the configuration CPP file
-(see for more details [http://forge.ipsl.jussieu.fr/nemo/wiki/Users "Learn more about the model"]).
+:file:`TRP`
+   Interface to NEMO physical core for computing tracers transport
+
+:file:`CFC`
+   Inert carbon tracers (CFC11,CFC12,SF6)
+
+:file:`C14`
+   Radiocarbon passive tracer
+
+:file:`AGE`
+   Water age tracking
+
+:file:`MY_TRC`
+   Template for creation of new modules and external BGC models coupling
+
+:file:`PISCES`
+   Built in BGC model. See :cite:`gmd-8-2465-2015` for a throughout description.
+
+The usage of TOP is activated
+*i)* by including in the configuration definition the component ``TOP`` and
+*ii)* by adding the macro ``key_top`` in the configuration CPP file
+(see for more details :forge:`"Learn more about the model" <wiki/Users>`).
 
 As an example, the user can refer to already available configurations in the code,
@@ -51 +56 @@
 (see also Section 4) .
 
-Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and
+Note that, since version 4.0,
+TOP interface core functionalities are activated by means of logical keys and
 all submodules preprocessing macros from previous versions were removed.
 
@@ -57 +63 @@
 
 ``key_iomput``
-   use XIOS I/O
+   use XIOS I/O
 
 ``key_agrif``
-   enable AGRIF coupling
+   enable AGRIF coupling
 
 ``key_trdtrc`` & ``key_trdmxl_trc``
-   trend computation for tracers
+   trend computation for tracers
 
 Synthetic Workflow
 ==================
 
-A synthetic description of the TOP interface workflow is given below to summarize the steps involved in
-the computation of biogeochemical and physical trends and their time integration and outputs,
+A synthetic description of the TOP interface workflow is given below to
+summarize the steps involved in the computation of biogeochemical and physical trends and
+their time integration and outputs,
 by reporting also the principal Fortran subroutine herein involved.
 
-**Model initialization (OPA_SRC/nemogcm.F90)**
-
-call to trc_init (trcini.F90)
-
-  ↳ call trc_nam (trcnam.F90) to initialize TOP tracers and run setting
-
-  ↳ call trc_ini_sms, to initialize each submodule
-
-  ↳ call trc_ini_trp, to initialize transport for tracers
-
-  ↳ call trc_ice_ini, to initialize tracers in seaice
-
-  ↳ call trc_ini_state, read passive tracers from a restart or input data
-
-  ↳ call trc_sub_ini, setup substepping if {{{nn_dttrc /= 1}}}
-
-**Time marching procedure (OPA_SRC/stp.F90)**
-
-call to trc_stp.F90 (trcstp.F90)
-
-  ↳ call trc_sub_stp, averaging physical variables for sub-stepping
-
-  ↳ call trc_wri, call XIOS for output of data
-
-  ↳ call trc_sms, compute BGC trends for each submodule
-
-    ↳ call trc_sms_my_trc, includes also surface and coastal BCs trends
-
-  ↳ call trc_trp (TRP/trctrp.F90), compute physical trends
-
-    ↳ call trc_sbc, get trend due to surface concentration/dilution
-
-    ↳ call trc_adv, compute tracers advection
-
-    ↳ call to trc_ldf, compute tracers lateral diffusion
-
-    ↳ call to trc_zdf, vertical mixing and after tracer fields
-
-    ↳ call to trc_nxt, tracer fields at next time step. Lateral Boundary Conditions are solved in here.
-
-    ↳ call to trc_rad, Correct artificial negative concentrations
-
-  ↳ call trc_rst_wri, output tracers restart files
+Model initialization (:file:`./src/OCE/nemogcm.F90`)
+----------------------------------------------------
+
+Call to ``trc_init`` subroutine (:file:`./src/TOP/trcini.F90`) to initialize TOP.
+
+.. literalinclude:: ../../../src/TOP/trcini.F90
+   :language:        fortran
+   :lines:           41-86
+   :emphasize-lines: 21,30-32,38-40
+   :caption:         ``trc_init`` subroutine
+
+Time marching procedure (:file:`./src/OCE/step.F90`)
+----------------------------------------------------
+
+Call to ``trc_stp`` subroutine (:file:`./src/TOP/trcstp.F90`) to compute/update passive tracers.
+
+.. literalinclude:: ../../../src/TOP/trcstp.F90
+   :language:        fortran
+   :lines:           46-125
+   :emphasize-lines: 42,55-57
+   :caption:         ``trc_stp`` subroutine
+
+BGC trends computation for each submodule (:file:`./src/TOP/trcsms.F90`)
+------------------------------------------------------------------------
+
+.. literalinclude:: ../../../src/TOP/trcsms.F90
+   :language:        fortran
+   :lines:           21
+   :caption:         :file:`trcsms` snippet
+
+Physical trends computation (:file:`./src/TOP/TRP/trctrp.F90`)
+--------------------------------------------------------------
+
+.. literalinclude:: ../../../src/TOP/TRP/trctrp.F90
+   :language:        fortran
+   :lines:           46-95
+   :emphasize-lines: 17,21,29,33-35
+   :caption:         ``trc_trp`` subroutine
 
 Namelists walkthrough
 =====================
 
-namelist_top
-------------
-
-Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and
-modifiable by means of namelist_top_cfg (as for NEMO physical ones).
-
-Note that ## is used to refer to a number in an array field.
+:file:`namelist_top`
+--------------------
+
+Here below are listed the features/options of the TOP interface accessible through
+the :file:`namelist_top_ref` and modifiable by means of :file:`namelist_top_cfg`
+(as for NEMO physical ones).
+
+Note that ``##`` is used to refer to a number in an array field.
 
 .. literalinclude:: ../../namelists/namtrc_run
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_dta
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_adv
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_ldf
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_rad
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_snk
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_dmp
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_ice
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_trd
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_bc
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namtrc_bdy
+   :language: fortran
 
 .. literalinclude:: ../../namelists/namage
-
-Two main types of data structure are used within TOP interface to initialize tracer properties (1) and
+   :language: fortran
+
+Two main types of data structure are used within TOP interface
+to initialize tracer properties (1) and
 to provide related initial and boundary conditions (2).
 
-**1. TOP tracers initialization**: sn_tracer (namtrc)
+1. TOP tracers initialization: ``sn_tracer`` (``&namtrc``)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Beside providing name and metadata for tracers,
-here are also defined the use of initial ({{{sn_tracer%llinit}}}) and
-boundary ({{{sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc}}}) conditions.
-
-In the following, an example of the full structure definition is given for two idealized tracers both with
-initial conditions given, while the first has only surface boundary forcing and
+here are also defined the use of initial (``sn_tracer%llinit``) and
+boundary (``sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc``) conditions.
+
+In the following, an example of the full structure definition is given for
+two idealized tracers both with initial conditions given,
+while the first has only surface boundary forcing and
 the second both surface and coastal forcings:
 
 .. code-block:: fortran
 
-   !             !    name   !           title of the field            !   units    ! initial data ! sbc   !   cbc  !   obc  !
-   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,  .true.      , .true., .false., .true.
-   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,  .true.      , .true., .true. , .false.
+   !             !    name   !           title of the field            !   units    ! initial data ! sbc   !   cbc  !   obc  !
+   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,  .true.      , .true., .false., .true.
+   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,  .true.      , .true., .true. , .false.
 
 As tracers in BGC models are increasingly growing,
@@ -177 +196 @@
 .. code-block:: fortran
 
-   !             !    name   !           title of the field            !   units    ! initial data !
-   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,   .true.
-   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,   .true.
-   ! sbc
-   sn_tracer(1)%llsbc = .true.
-   sn_tracer(2)%llsbc = .true.
-   ! cbc
-   sn_tracer(2)%llcbc = .true.
+   !             !    name   !           title of the field            !   units    ! initial data !
+   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,   .true.
+   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,   .true.
+   ! sbc
+   sn_tracer(1)%llsbc = .true.
+   sn_tracer(2)%llsbc = .true.
+   ! cbc
+   sn_tracer(2)%llcbc = .true.
 
 The data structure is internally initialized by code with dummy names and
-all initialization/forcing logical fields set to .false. .
-
-**2. Structures to read input initial and boundary conditions**: namtrc_dta (sn_trcdta), namtrc_bc (sn_trcsbc/sn_trccbc/sn_trcobc)
+all initialization/forcing logical fields set to ``.false.`` .
+
+2. Structures to read input initial and boundary conditions: ``&namtrc_dta`` (``sn_trcdta``), ``&namtrc_bc`` (``sn_trcsbc`` / ``sn_trccbc`` / ``sn_trcobc``)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The overall data structure (Fortran type) is based on the general one defined for NEMO core in the SBC component
-(see details in User Manual SBC Chapter on Input Data specification).
-
-Input fields are prescribed within namtrc_dta (with sn_trcdta structure),
-while Boundary Conditions are applied to the model by means of namtrc_bc,
-with dedicated structure fields for surface (sn_trcsbc), riverine (sn_trccbc), and
-lateral open (sn_trcobc) boundaries.
+(see details in ``SBC`` Chapter of :doc:`Reference Manual <cite>` on Input Data specification).
+
+Input fields are prescribed within ``&namtrc_dta`` (with ``sn_trcdta`` structure),
+while Boundary Conditions are applied to the model by means of ``&namtrc_bc``,
+with dedicated structure fields for surface (``sn_trcsbc``), riverine (``sn_trccbc``), and
+lateral open (``sn_trcobc``) boundaries.
 
 The following example illustrates the data structure in the case of initial condition for
-a single tracer contained in the file named tracer_1_data.nc (.nc is implicitly assumed in namelist filename),
-with a doubled initial value, and located in the usr/work/model/inputdata/ folder:
+a single tracer contained in the file named :file:`tracer_1_data.nc`
+(``.nc`` is implicitly assumed in namelist filename),
+with a doubled initial value, and located in the :file:`usr/work/model/inputdata` folder:
 
 .. code-block:: fortran
 
-   !               !  file name             ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-   !               !                        !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-     sn_trcdta(1)  = 'tracer_1_data'        ,        -12        ,  'TRC1'   ,    .false.   , .true. , 'yearly'  , ''       , ''       , ''
-     rf_trfac(1) = 2.0
-     cn_dir = “usr/work/model/inputdata/”
-
-Note that, the Lateral Open Boundaries conditions are applied on the segments defined for the physical core of NEMO
-(see BDY description in the User Manual).
-
-namelist_trc
-------------
-
-Here below the description of namelist_trc_ref used to handle Carbon tracers modules, namely CFC and C14.
-
-|||| &'''namcfc'''     !   CFC ||
-
-|||| &'''namc14_typ'''     !  C14 - type of C14 tracer, default values of C14/C and pco2 ||
-
-|||| &'''namc14_sbc'''     !  C14 - surface BC ||
-
-|||| &'''namc14_fcg'''     !  files & dates ||
+   !               !  file name             ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+   !               !                        !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+     sn_trcdta(1)  = 'tracer_1_data'        ,        -12        ,  'TRC1'   ,    .false.   , .true. , 'yearly'  , ''       , ''       , ''
+     rf_trfac(1) = 2.0
+     cn_dir = 'usr/work/model/inputdata/'
+
+Note that, the Lateral Open Boundaries conditions are applied on
+the segments defined for the physical core of NEMO
+(see ``BDY`` description in the :doc:`Reference Manual <cite>`).
+
+:file:`namelist_trc`
+--------------------
+
+Here below the description of :file:`namelist_trc_ref` used to handle Carbon tracers modules,
+namely CFC and C14.
+
+.. literalinclude:: ../../../cfgs/SHARED/namelist_trc_ref
+   :language: fortran
+   :lines: 7,17,26,34
+   :caption: :file:`namelist_trc_ref` snippet
 
 ``MY_TRC`` interface for coupling external BGC models
 =====================================================
 
-The generalized interface is pivoted on MY_TRC module that contains template files to build the coupling between
+The generalized interface is pivoted on MY_TRC module that contains template files to
+build the coupling between
 NEMO and any external BGC model.
 
-The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in namtrc)
+The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in ``&namtrc``)
 
 The following 6 fortran files are available in MY_TRC with the specific purposes here described.
 
-``par_my_trc.F90``
-   This module allows to define additional arrays and public variables to be used within the MY_TRC interface
-
-``trcini_my_trc.F90``
-   Here are initialized user defined namelists and the call to the external BGC model initialization procedures to
-   populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to
-   system metrics that could be needed by the BGC model.
-
-``trcnam_my_trc.F90``
-   This routine is called at the beginning of trcini_my_trc and should contain the initialization of
-   additional namelists for the BGC model or user-defined code.
-
-``trcsms_my_trc.F90``
-   The routine performs the call to Boundary Conditions and its main purpose is to
-   contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model.
-   Be aware that lateral boundary conditions are applied in trcnxt routine.
-   IMPORTANT: the routines to compute the light penetration along the water column and
-   the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in
-   the code.
-
-``trcice_my_trc.F90``
-   Here it is possible to prescribe the tracers concentrations in the seaice that will be used as
-   boundary conditions when ice melting occurs (nn_ice_tr =1 in namtrc_ice).
-   See e.g. the correspondent PISCES subroutine.
-
-``trcwri_my_trc.F90``
-   This routine performs the output of the model tracers (only those defined in namtrc) using IOM module
-   (see Manual Chapter “Output and Diagnostics”).
-   It is possible to place here the output of additional variables produced by the model,
-   if not done elsewhere in the code, using the call to iom_put.
+:file:`par_my_trc.F90`
+   This module allows to define additional arrays and public variables to
+   be used within the MY_TRC interface
+
+:file:`trcini_my_trc.F90`
+   Here are initialized user defined namelists and
+   the call to the external BGC model initialization procedures to populate general tracer array
+   (``trn`` and ``trb``).
+   Here are also likely to be defined support arrays related to system metrics that
+   could be needed by the BGC model.
+
+:file:`trcnam_my_trc.F90`
+   This routine is called at the beginning of ``trcini_my_trc`` and
+   should contain the initialization of additional namelists for the BGC model or user-defined code.
+
+:file:`trcsms_my_trc.F90`
+   The routine performs the call to Boundary Conditions and its main purpose is to
+   contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model.
+   Be aware that lateral boundary conditions are applied in trcnxt routine.
+
+   .. warning::
+      The routines to compute the light penetration along the water column and
+      the tracer vertical sinking should be defined/called in here,
+      as generalized modules are still missing in the code.
+
+:file:`trcice_my_trc.F90`
+   Here it is possible to prescribe the tracers concentrations in the sea-ice that
+   will be used as boundary conditions when ice melting occurs (``nn_ice_tr = 1`` in ``&namtrc_ice``).
+   See e.g. the correspondent PISCES subroutine.
+
+:file:`trcwri_my_trc.F90`
+   This routine performs the output of the model tracers (only those defined in ``&namtrc``) using
+   IOM module (see chapter “Output and Diagnostics” in the :doc:`Reference Manual <cite>`).
+   It is possible to place here the output of additional variables produced by the model,
+   if not done elsewhere in the code, using the call to ``iom_put``.
 
 Coupling an external BGC model using NEMO framework
@@ -273 +299 @@
 The coupling with an external BGC model through the NEMO compilation framework can be achieved in
 different ways according to the degree of coding complexity of the Biogeochemical model, like e.g.,
-the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders.
-
-Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and constituted by
-a rather essential coding structure, likely few Fortran files.
+the whole code is made only by one file or
+it has multiple modules and interfaces spread across several subfolders.
+
+Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and
+constituted by a rather essential coding structure, likely few Fortran files.
 The new coupled configuration name is *NEMO_MYBGC*.
 
-The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones) placed in
-a unique folder with root ``MYBGCPATH`` and to use the makenemo external readdressing of ``MY_SRC`` folder.
-
-The coupled configuration listed in ``work_cfgs.txt`` will look like
+The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones)
+placed in a unique folder with root ``MYBGCPATH`` and
+to use the makenemo external readdressing of ``MY_SRC`` folder.
+
+The coupled configuration listed in :file:`work_cfgs.txt` will look like
 
 ::
 
-   NEMO_MYBGC OPA_SRC TOP_SRC
+   NEMO_MYBGC OCE TOP
 
 and the related ``cpp_MYBGC.fcm`` content will be
@@ -292 +320 @@
 .. code-block:: perl
 
-   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
-
-the compilation with ``makenemo`` will be executed through the following syntax
+   bld::tool::fppkeys key_iomput key_mpp_mpi key_top
+
+the compilation with :file:`makenemo` will be executed through the following syntax
 
 .. code-block:: console
 
-   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>'
-
-The makenemo feature “-e” was introduced to readdress at compilation time the standard MY_SRC folder
-(usually found in NEMO configurations) with a user defined external one.
-
-The compilation of more articulated BGC model code & infrastructure, like in the case of BFM
-([http://www.bfm-community.eu/publications/bfmnemomanual_r1.0_201508.pdf BFM-NEMO coupling manual]),
-requires some additional features.
+   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>'
+
+The makenemo feature ``-e`` was introduced to
+readdress at compilation time the standard MY_SRC folder (usually found in NEMO configurations) with
+a user defined external one.
+
+The compilation of more articulated BGC model code & infrastructure,
+like in the case of BFM (|BFM man|_), requires some additional features.
 
 As before, let’s assume a coupled configuration name *NEMO_MYBGC*,
-but in this case MYBGC model root becomes ``<MYBGCPATH>`` that contains 4 different subfolders for
-biogeochemistry, named ``initialization``, ``pelagic``, and ``benthic``, and
-a separate one named ``nemo_coupling`` including the modified ``MY_SRC`` routines.
+but in this case MYBGC model root becomes :file:`MYBGC` path that
+contains 4 different subfolders for biogeochemistry,
+named :file:`initialization`, :file:`pelagic`, and :file:`benthic`,
+and a separate one named :file:`nemo_coupling` including the modified `MY_SRC` routines.
 The latter folder containing the modified NEMO coupling interface will be still linked using
-the makenemo “-e” option.
+the makenemo ``-e`` option.
 
 In order to include the BGC model subfolders in the compilation of NEMO code,
-it will be necessary to extend the configuration ``cpp_NEMO_MYBGC.fcm`` file to include the specific paths of
-``MYBGC`` folders, as in the following example
+it will be necessary to extend the configuration :file:`cpp_NEMO_MYBGC.fcm` file to include the specific paths of :file:`MYBGC` folders, as in the following example
 
 .. code-block:: perl
 
-   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
-   
-   src::MYBGC::initialization         <MYBGCPATH>/initialization
-   src::MYBGC::pelagic                <MYBGCPATH>/pelagic
-   src::MYBGC::benthic                <MYBGCPATH>/benthic
-   
-   bld::pp::MYBGC      1
-   bld::tool::fppflags::MYBGC   %FPPFLAGS
-   bld::tool::fppkeys           %bld::tool::fppkeys MYBGC_MACROS
+   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
+
+   src::MYBGC::initialization         <MYBGCPATH>/initialization
+   src::MYBGC::pelagic                <MYBGCPATH>/pelagic
+   src::MYBGC::benthic                <MYBGCPATH>/benthic
+
+   bld::pp::MYBGC      1
+   bld::tool::fppflags::MYBGC   %FPPFLAGS
+   bld::tool::fppkeys           %bld::tool::fppkeys MYBGC_MACROS
 
 where *MYBGC_MACROS* is the space delimited list of macros used in *MYBGC* model for
 selecting/excluding specific parts of the code.
-The BGC model code will be preprocessed in the configuration ``BLD`` folder as for NEMO,
-but with an independent path, like ``NEMO_MYBGC/BLD/MYBGC/<subforlders>``.
+The BGC model code will be preprocessed in the configuration :file:`BLD` folder as for NEMO,
+but with an independent path, like :file:`NEMO_MYBGC/BLD/MYBGC/<subforlders>`.
 
 The compilation will be performed similarly to in the previous case with the following
@@ -339 +367 @@
 .. code-block:: console
 
-   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling'
-
-Note that, the additional lines specific for the BGC model source and build paths can be written into
-a separate file, e.g. named ``MYBGC.fcm``, and then simply included in the ``cpp_NEMO_MYBGC.fcm`` as follow
-
-.. code-block:: perl
-
-   bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top
-   inc <MYBGCPATH>/MYBGC.fcm
-
-This will enable a more portable compilation structure for all MYBGC related configurations.
-
-**Important**: the coupling interface contained in nemo_coupling cannot be added using the FCM syntax,
-as the same files already exists in NEMO and they are overridden only with the readdressing of MY_SRC contents to
-avoid compilation conflicts due to duplicate routines.
-
-All modifications illustrated above, can be easily implemented using shell or python scripting to
-edit the NEMO configuration CPP.fcm file and to create the BGC model specific FCM compilation file with code paths.
+   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling'
+
+.. note::
+   The additional lines specific for the BGC model source and build paths can be written into
+   a separate file, e.g. named :file:`MYBGC.fcm`,
+   and then simply included in the :file:`cpp_NEMO_MYBGC.fcm` as follow
+
+   .. code-block:: perl
+
+      bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top
+      inc <MYBGCPATH>/MYBGC.fcm
+
+   This will enable a more portable compilation structure for all MYBGC related configurations.
+
+.. warning::
+   The coupling interface contained in :file:`nemo_coupling` cannot be added using the FCM syntax,
+   as the same files already exists in NEMO and they are overridden only with
+   the readdressing of MY_SRC contents to avoid compilation conflicts due to duplicate routines.
+
+All modifications illustrated above, can be easily implemented using shell or python scripting
+to edit the NEMO configuration :file:`CPP.fcm` file and
+to create the BGC model specific FCM compilation file with code paths.
+
+.. |BFM man| replace:: BFM-NEMO coupling manual